[Debian-med-packaging] Bug#733352: help needed for #733352

[Alex Mestiashvili]

On 04/11/2014 12:29 AM, Diane Trout wrote:
> On Thursday, April 10, 2014 15:30:21 Alex Mestiashvili wrote:
>> Dear mentors,
>>
>> I would greatly appreciate if somebody would help with the #733352, I've
>> spent a couple of hours trying to resolve the issue but my cpp skills
>> are rather poor.
>>
>> Thank you,
>> Alex
> The patch below deals with one of the compile errors. I don't know if just
> hiding the const modifier is better than pushing const-ness further into
> tophat.
>
> Unfortunately the next const error I get is even worse. Const-ness seems to
> get flipped between appendValue and trying to create a seqan::Gaps...
>
> Diane
>
>
> diff --git a/src/segment_juncs.cpp b/src/segment_juncs.cpp
> index e3acc46..d73e0d6 100644
> --- a/src/segment_juncs.cpp
> +++ b/src/segment_juncs.cpp
> @@ -2056,8 +2056,8 @@ void juncs_from_ref_segs(RefSequenceTable& rt,
>   
>       MotifMap ims;
>   
> -    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
> -    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
> +    seqan::DnaStringReverseComplement
> rev_donor_dinuc(const_cast<DnaString&>(donor_dinuc));
> +    seqan::DnaStringReverseComplement
> rev_acceptor_dinuc(const_cast<DnaString&>(acceptor_dinuc));
>   
>       if (talkative)
>           fprintf(stderr, "Collecting potential splice sites in islands\n");
>
>
>

Hi Diane,

Cool, thank you a lot, we are one step further!
Still I think that the upstream should try to fix it or we should 
reintroduce back SeqAn-1.3.

Best regards,
Alex